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<!-- ============================== header ================================= -->	
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<!-- ============================== classes index ============================ -->
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			<!-- begin publish.classesIndex -->
			<div align="center"><a href="../index.html">Class Index</a>
| <a href="../files.html">File Index</a></div>
<hr />
<h2>Classes</h2>
<ul class="classList">
	
	<li><i><a href="../symbols/_global_.html">_global_</a></i></li>
	
</ul>
<hr />
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		</div>
		
		<div id="content">
<!-- ============================== class title ============================ -->
			<h1 class="classTitle">
				
				Built-In Namespace _global_
			</h1>

<!-- ============================== class summary ========================== -->			
			<p class="description">
				
				
			
				
				
				
			</p>

<!-- ============================== constructor summary ==================== -->			
			

<!-- ============================== properties summary ===================== -->
			
				
				
				<table class="summaryTable" cellspacing="0" summary="A summary of the fields documented in the class _global_.">
					<caption>Field Summary</caption>
					<thead>
						<tr>
							<th scope="col">Field Attributes</th>
							<th scope="col">Field Name and Description</th>
						</tr>
					</thead>
					<tbody>
					
						<tr>
							<td class="attributes">&nbsp;</td>
							<td class="nameDescription">
								<div class="fixedFont">
								<b><a href="../symbols/_global_.html#o">o</a></b>
								</div>
								<div class="description"></div>
							</td>
						</tr>
					
						<tr>
							<td class="attributes">&nbsp;</td>
							<td class="nameDescription">
								<div class="fixedFont">
								<b><a href="../symbols/_global_.html#rgraph">rgraph</a></b>
								</div>
								<div class="description">config.js - Initializes all globals and the config dict.</div>
							</td>
						</tr>
					
					</tbody>
				</table>
				
				
				
			

<!-- ============================== methods summary ======================== -->
			
				
				
				<table class="summaryTable" cellspacing="0" summary="A summary of the methods documented in the class _global_.">
					<caption>Method Summary</caption>
					<thead>
						<tr>
							<th scope="col">Method Attributes</th>
							<th scope="col">Method Name and Description</th>
						</tr>
					</thead>
					<tbody>
					
						<tr>
							<td class="attributes">&nbsp;</td>
							<td class="nameDescription">
								<div class="fixedFont"><b><a href="../symbols/_global_.html#addSavedViewToList">addSavedViewToList</a></b>(id, name)
								</div>
								<div class="description">Adds the views name and load-, delete-, and export-buttons to the left navigation with their css-styles.</div>
							</td>
						</tr>
					
						<tr>
							<td class="attributes">&nbsp;</td>
							<td class="nameDescription">
								<div class="fixedFont"><b><a href="../symbols/_global_.html#alignmentfunction">alignmentfunction</a></b>(thisid, nodeFrom, nodeTo)
								</div>
								<div class="description">Function for showing the alignment of the read and the db-entry and coloring it so that you can easily see which parts match</div>
							</td>
						</tr>
					
						<tr>
							<td class="attributes">&nbsp;</td>
							<td class="nameDescription">
								<div class="fixedFont"><b><a href="../symbols/_global_.html#checkRootTagpath">checkRootTagpath</a></b>(node)
								</div>
								<div class="description">Function for checking if node has a tagged path to the root node.</div>
							</td>
						</tr>
					
						<tr>
							<td class="attributes">&nbsp;</td>
							<td class="nameDescription">
								<div class="fixedFont"><b><a href="../symbols/_global_.html#cleanupGraph">cleanupGraph</a></b>()
								</div>
								<div class="description">clean up the graph by removing leftover stuff
(e.g.</div>
							</td>
						</tr>
					
						<tr>
							<td class="attributes">&nbsp;</td>
							<td class="nameDescription">
								<div class="fixedFont"><b><a href="../symbols/_global_.html#closealignment">closealignment</a></b>(button)
								</div>
								<div class="description">Function to close and delete the div-element showing the alignment</div>
							</td>
						</tr>
					
						<tr>
							<td class="attributes">&nbsp;</td>
							<td class="nameDescription">
								<div class="fixedFont"><b><a href="../symbols/_global_.html#closeSearch">closeSearch</a></b>(e)
								</div>
								<div class="description">Closes the left side query menu.</div>
							</td>
						</tr>
					
						<tr>
							<td class="attributes">&nbsp;</td>
							<td class="nameDescription">
								<div class="fixedFont"><b><a href="../symbols/_global_.html#colorEdges">colorEdges</a></b>()
								</div>
								<div class="description">Calculates colors for all adges and nodes in the graph and add that information
in the nodes and edges.</div>
							</td>
						</tr>
					
						<tr>
							<td class="attributes">&nbsp;</td>
							<td class="nameDescription">
								<div class="fixedFont"><b><a href="../symbols/_global_.html#contractForTraversal">contractForTraversal</a></b>(node, opt)
								</div>
								<div class="description">Modified version of the original contract function for removing unnecessary
nodes while traversing the graph.</div>
							</td>
						</tr>
					
						<tr>
							<td class="attributes">&nbsp;</td>
							<td class="nameDescription">
								<div class="fixedFont"><b><a href="../symbols/_global_.html#deleteByBitscore">deleteByBitscore</a></b>(bitscoreLimit)
								</div>
								<div class="description">not used</div>
							</td>
						</tr>
					
						<tr>
							<td class="attributes">&nbsp;</td>
							<td class="nameDescription">
								<div class="fixedFont"><b><a href="../symbols/_global_.html#deleteUntagged">deleteUntagged</a></b>(bitscoreLimit)
								</div>
								<div class="description">Function for deleting nodes from the graph.</div>
							</td>
						</tr>
					
						<tr>
							<td class="attributes">&nbsp;</td>
							<td class="nameDescription">
								<div class="fixedFont"><b><a href="../symbols/_global_.html#dotLineLength">dotLineLength</a></b>(x, y, x0, y0, x1, y1, o)
								</div>
								<div class="description">Calculate the shortest distance between a line segment and a point</div>
							</td>
						</tr>
					
						<tr>
							<td class="attributes">&nbsp;</td>
							<td class="nameDescription">
								<div class="fixedFont"><b><a href="../symbols/_global_.html#doUndo">doUndo</a></b>()
								</div>
								<div class="description">If there are saved states to use for undoing, morphs the graph into the last state recorded.</div>
							</td>
						</tr>
					
						<tr>
							<td class="attributes">&nbsp;</td>
							<td class="nameDescription">
								<div class="fixedFont"><b><a href="../symbols/_global_.html#fetchJSON">fetchJSON</a></b>(node)
								</div>
								<div class="description">expand the graph at the specified node</div>
							</td>
						</tr>
					
						<tr>
							<td class="attributes">&nbsp;</td>
							<td class="nameDescription">
								<div class="fixedFont"><b><a href="../symbols/_global_.html#filter">filter</a></b>(bitscore)
								</div>
								<div class="description">Function to filter graph based on a bitscore given by the user.</div>
							</td>
						</tr>
					
						<tr>
							<td class="attributes">&nbsp;</td>
							<td class="nameDescription">
								<div class="fixedFont"><b><a href="../symbols/_global_.html#hideCtxMenu">hideCtxMenu</a></b>()
								</div>
								<div class="description">Called when the context menu is being hidden</div>
							</td>
						</tr>
					
						<tr>
							<td class="attributes">&nbsp;</td>
							<td class="nameDescription">
								<div class="fixedFont"><b><a href="../symbols/_global_.html#hsvToRgb">hsvToRgb</a></b>(Number, Number, Number)
								</div>
								<div class="description">http://mjijackson.com/2008/02/rgb-to-hsl-and-rgb-to-hsv-color-model-conversion-algorithms-in-javascript
Converts an HSV color value to RGB.</div>
							</td>
						</tr>
					
						<tr>
							<td class="attributes">&nbsp;</td>
							<td class="nameDescription">
								<div class="fixedFont"><b><a href="../symbols/_global_.html#initContextMenu">initContextMenu</a></b>()
								</div>
								<div class="description">Adds the context menu to the canvas and binds all the necessary events.</div>
							</td>
						</tr>
					
						<tr>
							<td class="attributes">&nbsp;</td>
							<td class="nameDescription">
								<div class="fixedFont"><b><a href="../symbols/_global_.html#initGraph">initGraph</a></b>()
								</div>
								<div class="description">This function creates the graph according to the JSON data.</div>
							</td>
						</tr>
					
						<tr>
							<td class="attributes">&nbsp;</td>
							<td class="nameDescription">
								<div class="fixedFont"><b><a href="../symbols/_global_.html#openSearch">openSearch</a></b>()
								</div>
								<div class="description">Opens the left side query menu.</div>
							</td>
						</tr>
					
						<tr>
							<td class="attributes">&nbsp;</td>
							<td class="nameDescription">
								<div class="fixedFont"><b><a href="../symbols/_global_.html#prepareJSON">prepareJSON</a></b>(json)
								</div>
								<div class="description">prepareJSON(jitJSON json) - prepare a JIT graph in JSON 'graph' form for display</div>
							</td>
						</tr>
					
						<tr>
							<td class="attributes">&nbsp;</td>
							<td class="nameDescription">
								<div class="fixedFont"><b><a href="../symbols/_global_.html#saveUndoState">saveUndoState</a></b>()
								</div>
								<div class="description">Deep copies and saves the new state of the graph into undoStates.</div>
							</td>
						</tr>
					
						<tr>
							<td class="attributes">&nbsp;</td>
							<td class="nameDescription">
								<div class="fixedFont"><b><a href="../symbols/_global_.html#setBitscoreColoring">setBitscoreColoring</a></b>(min, max)
								</div>
								<div class="description">Sets bitscorelimits based on the given arguments and color the graph.</div>
							</td>
						</tr>
					
						<tr>
							<td class="attributes">&nbsp;</td>
							<td class="nameDescription">
								<div class="fixedFont"><b><a href="../symbols/_global_.html#setBusy">setBusy</a></b>(msg)
								</div>
								<div class="description">setBusy(null|string msg) - Set animation busy status
If msg is a string, add a loading bar with the specified message and prevent all other operations
If msg is null, disable busy state</div>
							</td>
						</tr>
					
						<tr>
							<td class="attributes">&nbsp;</td>
							<td class="nameDescription">
								<div class="fixedFont"><b><a href="../symbols/_global_.html#showEnzymeData">showEnzymeData</a></b>(json)
								</div>
								<div class="description">Function to list all names, reactions and pathways related to an enzyme in the right container.</div>
							</td>
						</tr>
					
						<tr>
							<td class="attributes">&nbsp;</td>
							<td class="nameDescription">
								<div class="fixedFont"><b><a href="../symbols/_global_.html#tagNode">tagNode</a></b>(node)
								</div>
								<div class="description">Function for tagging a node.</div>
							</td>
						</tr>
					
						<tr>
							<td class="attributes">&nbsp;</td>
							<td class="nameDescription">
								<div class="fixedFont"><b><a href="../symbols/_global_.html#tagParents">tagParents</a></b>(node)
								</div>
								<div class="description">Function for tagging a path from node to root.</div>
							</td>
						</tr>
					
						<tr>
							<td class="attributes">&nbsp;</td>
							<td class="nameDescription">
								<div class="fixedFont"><b><a href="../symbols/_global_.html#tagSubgraph">tagSubgraph</a></b>(node)
								</div>
								<div class="description">Tags the subgraph of the node</div>
							</td>
						</tr>
					
						<tr>
							<td class="attributes">&nbsp;</td>
							<td class="nameDescription">
								<div class="fixedFont"><b><a href="../symbols/_global_.html#tagSubnodes">tagSubnodes</a></b>(node)
								</div>
								<div class="description">Tags the subnodes of the node</div>
							</td>
						</tr>
					
						<tr>
							<td class="attributes">&nbsp;</td>
							<td class="nameDescription">
								<div class="fixedFont"><b><a href="../symbols/_global_.html#untagNode">untagNode</a></b>(node)
								</div>
								<div class="description">Untags a node.</div>
							</td>
						</tr>
					
						<tr>
							<td class="attributes">&nbsp;</td>
							<td class="nameDescription">
								<div class="fixedFont"><b><a href="../symbols/_global_.html#untagSubgraph">untagSubgraph</a></b>(node)
								</div>
								<div class="description">Untags a subgraph</div>
							</td>
						</tr>
					
						<tr>
							<td class="attributes">&nbsp;</td>
							<td class="nameDescription">
								<div class="fixedFont"><b><a href="../symbols/_global_.html#updateBitscores">updateBitscores</a></b>()
								</div>
								<div class="description">Function for updating data.bitscore field for all nodes in the graph.</div>
							</td>
						</tr>
					
					</tbody>
				</table>
				
				
				
			
<!-- ============================== events summary ======================== -->
			

<!-- ============================== constructor details ==================== -->		
			

<!-- ============================== field details ========================== -->		
			
				<div class="sectionTitle">
					Field Detail
				</div>
				
					<a name="o"> </a>
					<div class="fixedFont">
					
					
					<b>o</b>
					
					</div>
					<div class="description">
						
						
							<br />
							<i>Defined in: </i> <a href="../symbols/src/geovision_src_geovision_static_js_styles.js.html">styles.js</a>.
						
						
					</div>
					
					

						
						
						
						

					<hr />
				
					<a name="rgraph"> </a>
					<div class="fixedFont">
					
					
					<b>rgraph</b>
					
					</div>
					<div class="description">
						config.js - Initializes all globals and the config dict. Sets default
values for settings. Detailed explanation of all the configurations available
e.g. for animations can be found at the JIT documents page
http://thejit.org/static/v20/Docs/.
						
							<br />
							<i>Defined in: </i> <a href="../symbols/src/geovision_src_geovision_static_js_config.js.html">config.js</a>.
						
						
					</div>
					
					

						
						
						
						

					
				
			

<!-- ============================== method details ========================= -->		
			
				<div class="sectionTitle">
					Method Detail
				</div>
				
					<a name="addSavedViewToList"> </a>
					<div class="fixedFont">
					
					
					<b>addSavedViewToList</b>(id, name)
					
					</div>
					<div class="description">
						Adds the views name and load-, delete-, and export-buttons to the left navigation with their css-styles.
						
							<br />
							<i>Defined in: </i> <a href="../symbols/src/geovision_src_geovision_static_js_loadsave.js.html">loadsave.js</a>.
						
						
					</div>
					
					
					
						
							<dl class="detailList">
							<dt class="heading">Parameters:</dt>
							
								<dt>
									<b>id</b>
									
								</dt>
								<dd>the id of the saved view in question</dd>
							
								<dt>
									<b>name</b>
									
								</dt>
								<dd>the name of the view</dd>
							
							</dl>
						
						
						
						
						
						
						

					<hr />
				
					<a name="alignmentfunction"> </a>
					<div class="fixedFont">
					
					
					<b>alignmentfunction</b>(thisid, nodeFrom, nodeTo)
					
					</div>
					<div class="description">
						Function for showing the alignment of the read and the db-entry and coloring it so that you can easily see which parts match
						
							<br />
							<i>Defined in: </i> <a href="../symbols/src/geovision_src_geovision_static_js_moreinfo.js.html">moreinfo.js</a>.
						
						
					</div>
					
					
					
						
							<dl class="detailList">
							<dt class="heading">Parameters:</dt>
							
								<dt>
									<b>thisid</b>
									
								</dt>
								<dd>the id of the edge for which the alignment is shown</dd>
							
								<dt>
									<b>nodeFrom</b>
									
								</dt>
								<dd>the id of the node on the other side of the edge, only used for showing to the user so it's easier to distinguish alignments from eachother</dd>
							
								<dt>
									<b>nodeTo</b>
									
								</dt>
								<dd>the id of the node on the other side of the edge, only used for showing to the user so it's easier to distinguish alignments from eachother</dd>
							
							</dl>
						
						
						
						
						
						
						

					<hr />
				
					<a name="checkRootTagpath"> </a>
					<div class="fixedFont">
					
					
					<b>checkRootTagpath</b>(node)
					
					</div>
					<div class="description">
						Function for checking if node has a tagged path to the root node.
Assumes the node has a path to root.
						
							<br />
							<i>Defined in: </i> <a href="../symbols/src/geovision_src_geovision_static_js_navigation.js.html">navigation.js</a>.
						
						
					</div>
					
					
					
						
							<dl class="detailList">
							<dt class="heading">Parameters:</dt>
							
								<dt>
									<b>node</b>
									
								</dt>
								<dd>the node for which to check the path</dd>
							
							</dl>
						
						
						
						
						
						
						

					<hr />
				
					<a name="cleanupGraph"> </a>
					<div class="fixedFont">
					
					
					<b>cleanupGraph</b>()
					
					</div>
					<div class="description">
						clean up the graph by removing leftover stuff
(e.g. edges with $alpha 0.0) that JIT tends to leave when deleting nodes.
						
							<br />
							<i>Defined in: </i> <a href="../symbols/src/geovision_src_geovision_static_js_graphviz.js.html">graphviz.js</a>.
						
						
					</div>
					
					
					
						
						
						
						
						
						
						

					<hr />
				
					<a name="closealignment"> </a>
					<div class="fixedFont">
					
					
					<b>closealignment</b>(button)
					
					</div>
					<div class="description">
						Function to close and delete the div-element showing the alignment
						
							<br />
							<i>Defined in: </i> <a href="../symbols/src/geovision_src_geovision_static_js_moreinfo.js.html">moreinfo.js</a>.
						
						
					</div>
					
					
					
						
							<dl class="detailList">
							<dt class="heading">Parameters:</dt>
							
								<dt>
									<b>button</b>
									
								</dt>
								<dd>the DOM-element which was clicked to start this function</dd>
							
							</dl>
						
						
						
						
						
						
						

					<hr />
				
					<a name="closeSearch"> </a>
					<div class="fixedFont">
					
					
					<b>closeSearch</b>(e)
					
					</div>
					<div class="description">
						Closes the left side query menu.
						
							<br />
							<i>Defined in: </i> <a href="../symbols/src/geovision_src_geovision_static_js_effects.js.html">effects.js</a>.
						
						
					</div>
					
					
					
						
							<dl class="detailList">
							<dt class="heading">Parameters:</dt>
							
								<dt>
									<b>e</b>
									
								</dt>
								<dd>the DOM-element triggering the event</dd>
							
							</dl>
						
						
						
						
						
						
						

					<hr />
				
					<a name="colorEdges"> </a>
					<div class="fixedFont">
					
					
					<b>colorEdges</b>()
					
					</div>
					<div class="description">
						Calculates colors for all adges and nodes in the graph and add that information
in the nodes and edges. Color can be accessed through node.data.$color.
						
							<br />
							<i>Defined in: </i> <a href="../symbols/src/geovision_src_geovision_static_js_bitscore.js.html">bitscore.js</a>.
						
						
					</div>
					
					
					
						
						
						
						
						
						
						

					<hr />
				
					<a name="contractForTraversal"> </a>
					<div class="fixedFont">
					
					
					<b>contractForTraversal</b>(node, opt)
					
					</div>
					<div class="description">
						Modified version of the original contract function for removing unnecessary
nodes while traversing the graph.
TODO: NOT USED
						
							<br />
							<i>Defined in: </i> <a href="../symbols/src/geovision_src_geovision_static_js_navigation.js.html">navigation.js</a>.
						
						
					</div>
					
					
					
						
							<dl class="detailList">
							<dt class="heading">Parameters:</dt>
							
								<dt>
									<b>node</b>
									
								</dt>
								<dd>node to contract the graph from</dd>
							
								<dt>
									<b>opt</b>
									
								</dt>
								<dd>options</dd>
							
							</dl>
						
						
						
						
						
						
						

					<hr />
				
					<a name="deleteByBitscore"> </a>
					<div class="fixedFont">
					
					
					<b>deleteByBitscore</b>(bitscoreLimit)
					
					</div>
					<div class="description">
						not used
						
							<br />
							<i>Defined in: </i> <a href="../symbols/src/geovision_src_geovision_static_js_navigation.js.html">navigation.js</a>.
						
						
					</div>
					
					
					
						
							<dl class="detailList">
							<dt class="heading">Parameters:</dt>
							
								<dt>
									<b>bitscoreLimit</b>
									
								</dt>
								<dd></dd>
							
							</dl>
						
						
						
						
						
						
						

					<hr />
				
					<a name="deleteUntagged"> </a>
					<div class="fixedFont">
					
					
					<b>deleteUntagged</b>(bitscoreLimit)
					
					</div>
					<div class="description">
						Function for deleting nodes from the graph.
If bitscoreLimit is not defined, all untagged nodes except root will be deleted.
If bitscoreLimit is defined, all untagged nodes (except root) without connections 
over that bitscore will be deleted. It will also preserve a path to root from each
remaining node (since many operations would break if graph became disconnected).

Function will also clean all edges to (and from) the deleted nodes from the graph, 
and update data.bitscore field for remaining nodes.

Will also untag all nodes once finished.
						
							<br />
							<i>Defined in: </i> <a href="../symbols/src/geovision_src_geovision_static_js_navigation.js.html">navigation.js</a>.
						
						
					</div>
					
					
					
						
							<dl class="detailList">
							<dt class="heading">Parameters:</dt>
							
								<dt>
									<b>bitscoreLimit</b>
									
								</dt>
								<dd>the limit under which nodes will be deleted</dd>
							
							</dl>
						
						
						
						
						
						
						

					<hr />
				
					<a name="dotLineLength"> </a>
					<div class="fixedFont">
					
					
					<b>dotLineLength</b>(x, y, x0, y0, x1, y1, o)
					
					</div>
					<div class="description">
						Calculate the shortest distance between a line segment and a point
						
							<br />
							<i>Defined in: </i> <a href="../symbols/src/geovision_src_geovision_static_js_styles.js.html">styles.js</a>.
						
						
					</div>
					
					
					
						
							<dl class="detailList">
							<dt class="heading">Parameters:</dt>
							
								<dt>
									<b>x</b>
									
								</dt>
								<dd></dd>
							
								<dt>
									<b>y</b>
									
								</dt>
								<dd></dd>
							
								<dt>
									<b>x0</b>
									
								</dt>
								<dd></dd>
							
								<dt>
									<b>y0</b>
									
								</dt>
								<dd></dd>
							
								<dt>
									<b>x1</b>
									
								</dt>
								<dd></dd>
							
								<dt>
									<b>y1</b>
									
								</dt>
								<dd></dd>
							
								<dt>
									<b>o</b>
									
								</dt>
								<dd></dd>
							
							</dl>
						
						
						
						
						
						
						

					<hr />
				
					<a name="doUndo"> </a>
					<div class="fixedFont">
					
					
					<b>doUndo</b>()
					
					</div>
					<div class="description">
						If there are saved states to use for undoing, morphs the graph into the last state recorded.
If there are no states, sets the undo-button to disabled.
						
							<br />
							<i>Defined in: </i> <a href="../symbols/src/geovision_src_geovision_static_js_loadsave.js.html">loadsave.js</a>.
						
						
					</div>
					
					
					
						
						
						
						
						
						
						

					<hr />
				
					<a name="fetchJSON"> </a>
					<div class="fixedFont">
					
					
					<b>fetchJSON</b>(node)
					
					</div>
					<div class="description">
						expand the graph at the specified node
						
							<br />
							<i>Defined in: </i> <a href="../symbols/src/geovision_src_geovision_static_js_graphviz.js.html">graphviz.js</a>.
						
						
					</div>
					
					
					
						
							<dl class="detailList">
							<dt class="heading">Parameters:</dt>
							
								<dt>
									<b>node</b>
									
								</dt>
								<dd>JitNode from which the graph needs to expand</dd>
							
							</dl>
						
						
						
						
						
						
						

					<hr />
				
					<a name="filter"> </a>
					<div class="fixedFont">
					
					
					<b>filter</b>(bitscore)
					
					</div>
					<div class="description">
						Function to filter graph based on a bitscore given by the user.
						
							<br />
							<i>Defined in: </i> <a href="../symbols/src/geovision_src_geovision_static_js_bitscore.js.html">bitscore.js</a>.
						
						
					</div>
					
					
					
						
							<dl class="detailList">
							<dt class="heading">Parameters:</dt>
							
								<dt>
									<b>bitscore</b>
									
								</dt>
								<dd>the bitscore to be used for filtering</dd>
							
							</dl>
						
						
						
						
						
						
						

					<hr />
				
					<a name="hideCtxMenu"> </a>
					<div class="fixedFont">
					
					
					<b>hideCtxMenu</b>()
					
					</div>
					<div class="description">
						Called when the context menu is being hidden
						
							<br />
							<i>Defined in: </i> <a href="../symbols/src/geovision_src_geovision_static_js_contextmenu.js.html">contextmenu.js</a>.
						
						
					</div>
					
					
					
						
						
						
						
						
						
						

					<hr />
				
					<a name="hsvToRgb"> </a>
					<div class="fixedFont">
					
					
					<b>hsvToRgb</b>(Number, Number, Number)
					
					</div>
					<div class="description">
						http://mjijackson.com/2008/02/rgb-to-hsl-and-rgb-to-hsv-color-model-conversion-algorithms-in-javascript
Converts an HSV color value to RGB. Conversion formula
adapted from http://en.wikipedia.org/wiki/HSV_color_space.
Assumes h, s, and v are contained in the set [0, 1] and
returns r, g, and b in the set [0, 255].
						
							<br />
							<i>Defined in: </i> <a href="../symbols/src/geovision_src_geovision_static_js_bitscore.js.html">bitscore.js</a>.
						
						
					</div>
					
					
					
						
							<dl class="detailList">
							<dt class="heading">Parameters:</dt>
							
								<dt>
									<b>Number</b>
									
								</dt>
								<dd>h       The hue</dd>
							
								<dt>
									<b>Number</b>
									
								</dt>
								<dd>s       The saturation</dd>
							
								<dt>
									<b>Number</b>
									
								</dt>
								<dd>v       The value</dd>
							
							</dl>
						
						
						
						
						
							<dl class="detailList">
							<dt class="heading">Returns:</dt>
							
								<dd>Array           The RGB representation</dd>
							
							</dl>
						
						
						

					<hr />
				
					<a name="initContextMenu"> </a>
					<div class="fixedFont">
					
					
					<b>initContextMenu</b>()
					
					</div>
					<div class="description">
						Adds the context menu to the canvas and binds all the necessary events.
The event bindings are done in the jquery-contextmenu plugin code
						
							<br />
							<i>Defined in: </i> <a href="../symbols/src/geovision_src_geovision_static_js_contextmenu.js.html">contextmenu.js</a>.
						
						
					</div>
					
					
					
						
						
						
						
						
						
						

					<hr />
				
					<a name="initGraph"> </a>
					<div class="fixedFont">
					
					
					<b>initGraph</b>()
					
					</div>
					<div class="description">
						This function creates the graph according to the JSON data.
						
							<br />
							<i>Defined in: </i> <a href="../symbols/src/geovision_src_geovision_static_js_graphviz.js.html">graphviz.js</a>.
						
						
					</div>
					
					
					
						
						
						
						
						
						
						

					<hr />
				
					<a name="openSearch"> </a>
					<div class="fixedFont">
					
					
					<b>openSearch</b>()
					
					</div>
					<div class="description">
						Opens the left side query menu.
						
							<br />
							<i>Defined in: </i> <a href="../symbols/src/geovision_src_geovision_static_js_effects.js.html">effects.js</a>.
						
						
					</div>
					
					
					
						
						
						
						
						
						
						

					<hr />
				
					<a name="prepareJSON"> </a>
					<div class="fixedFont">
					
					
					<b>prepareJSON</b>(json)
					
					</div>
					<div class="description">
						prepareJSON(jitJSON json) - prepare a JIT graph in JSON 'graph' form for display
						
							<br />
							<i>Defined in: </i> <a href="../symbols/src/geovision_src_geovision_static_js_graphviz.js.html">graphviz.js</a>.
						
						
					</div>
					
					
					
						
							<dl class="detailList">
							<dt class="heading">Parameters:</dt>
							
								<dt>
									<b>json</b>
									
								</dt>
								<dd>the json to be used for the graph</dd>
							
							</dl>
						
						
						
						
						
							<dl class="detailList">
							<dt class="heading">Returns:</dt>
							
								<dd>the 'graphified' json</dd>
							
							</dl>
						
						
						

					<hr />
				
					<a name="saveUndoState"> </a>
					<div class="fixedFont">
					
					
					<b>saveUndoState</b>()
					
					</div>
					<div class="description">
						Deep copies and saves the new state of the graph into undoStates.
If there are too many states, shifts the array. Also removes the undo-buttons disabled attribute if it has one.
						
							<br />
							<i>Defined in: </i> <a href="../symbols/src/geovision_src_geovision_static_js_loadsave.js.html">loadsave.js</a>.
						
						
					</div>
					
					
					
						
						
						
						
						
						
						

					<hr />
				
					<a name="setBitscoreColoring"> </a>
					<div class="fixedFont">
					
					
					<b>setBitscoreColoring</b>(min, max)
					
					</div>
					<div class="description">
						Sets bitscorelimits based on the given arguments and color the graph.
						
							<br />
							<i>Defined in: </i> <a href="../symbols/src/geovision_src_geovision_static_js_effects.js.html">effects.js</a>.
						
						
					</div>
					
					
					
						
							<dl class="detailList">
							<dt class="heading">Parameters:</dt>
							
								<dt>
									<b>min</b>
									
								</dt>
								<dd>minimum bitscore</dd>
							
								<dt>
									<b>max</b>
									
								</dt>
								<dd>maximum bitscore</dd>
							
							</dl>
						
						
						
						
						
						
						

					<hr />
				
					<a name="setBusy"> </a>
					<div class="fixedFont">
					
					
					<b>setBusy</b>(msg)
					
					</div>
					<div class="description">
						setBusy(null|string msg) - Set animation busy status
If msg is a string, add a loading bar with the specified message and prevent all other operations
If msg is null, disable busy state
						
							<br />
							<i>Defined in: </i> <a href="../symbols/src/geovision_src_geovision_static_js_graphviz.js.html">graphviz.js</a>.
						
						
					</div>
					
					
					
						
							<dl class="detailList">
							<dt class="heading">Parameters:</dt>
							
								<dt>
									<b>msg</b>
									
								</dt>
								<dd>message to be shown</dd>
							
							</dl>
						
						
						
						
						
						
						

					<hr />
				
					<a name="showEnzymeData"> </a>
					<div class="fixedFont">
					
					
					<b>showEnzymeData</b>(json)
					
					</div>
					<div class="description">
						Function to list all names, reactions and pathways related to an enzyme in the right container.
						
							<br />
							<i>Defined in: </i> <a href="../symbols/src/geovision_src_geovision_static_js_moreinfo.js.html">moreinfo.js</a>.
						
						
					</div>
					
					
					
						
							<dl class="detailList">
							<dt class="heading">Parameters:</dt>
							
								<dt>
									<b>json</b>
									
								</dt>
								<dd>the json to get info from</dd>
							
							</dl>
						
						
						
						
						
						
						

					<hr />
				
					<a name="tagNode"> </a>
					<div class="fixedFont">
					
					
					<b>tagNode</b>(node)
					
					</div>
					<div class="description">
						Function for tagging a node. If node has no tagged path to root, a path will also be tagged
since otherwise deletion could result in disconnected graph.
						
							<br />
							<i>Defined in: </i> <a href="../symbols/src/geovision_src_geovision_static_js_navigation.js.html">navigation.js</a>.
						
						
					</div>
					
					
					
						
							<dl class="detailList">
							<dt class="heading">Parameters:</dt>
							
								<dt>
									<b>node</b>
									
								</dt>
								<dd>the node to be tagged</dd>
							
							</dl>
						
						
						
						
						
						
						

					<hr />
				
					<a name="tagParents"> </a>
					<div class="fixedFont">
					
					
					<b>tagParents</b>(node)
					
					</div>
					<div class="description">
						Function for tagging a path from node to root.
Builds path by tagging the parent with the best (bitscore) connection to current node.
Responsibility for updating the visualization is left to user, this function does
not call refresh() or any animating function.
						
							<br />
							<i>Defined in: </i> <a href="../symbols/src/geovision_src_geovision_static_js_navigation.js.html">navigation.js</a>.
						
						
					</div>
					
					
					
						
							<dl class="detailList">
							<dt class="heading">Parameters:</dt>
							
								<dt>
									<b>node</b>
									
								</dt>
								<dd>the node which will have its parents tagged</dd>
							
							</dl>
						
						
						
						
						
						
						

					<hr />
				
					<a name="tagSubgraph"> </a>
					<div class="fixedFont">
					
					
					<b>tagSubgraph</b>(node)
					
					</div>
					<div class="description">
						Tags the subgraph of the node
						
							<br />
							<i>Defined in: </i> <a href="../symbols/src/geovision_src_geovision_static_js_navigation.js.html">navigation.js</a>.
						
						
					</div>
					
					
					
						
							<dl class="detailList">
							<dt class="heading">Parameters:</dt>
							
								<dt>
									<b>node</b>
									
								</dt>
								<dd>target node to have its subgraph tagged</dd>
							
							</dl>
						
						
						
						
						
						
						

					<hr />
				
					<a name="tagSubnodes"> </a>
					<div class="fixedFont">
					
					
					<b>tagSubnodes</b>(node)
					
					</div>
					<div class="description">
						Tags the subnodes of the node
						
							<br />
							<i>Defined in: </i> <a href="../symbols/src/geovision_src_geovision_static_js_navigation.js.html">navigation.js</a>.
						
						
					</div>
					
					
					
						
							<dl class="detailList">
							<dt class="heading">Parameters:</dt>
							
								<dt>
									<b>node</b>
									
								</dt>
								<dd>target node to have subnodes tagged</dd>
							
							</dl>
						
						
						
						
						
						
						

					<hr />
				
					<a name="untagNode"> </a>
					<div class="fixedFont">
					
					
					<b>untagNode</b>(node)
					
					</div>
					<div class="description">
						Untags a node.
Since many operations rely on all nodes having a path to root, also untags all
tagged nodes without a tagged path to root after untagging this node.
						
							<br />
							<i>Defined in: </i> <a href="../symbols/src/geovision_src_geovision_static_js_navigation.js.html">navigation.js</a>.
						
						
					</div>
					
					
					
						
							<dl class="detailList">
							<dt class="heading">Parameters:</dt>
							
								<dt>
									<b>node</b>
									
								</dt>
								<dd>node to be untagged</dd>
							
							</dl>
						
						
						
						
						
						
						

					<hr />
				
					<a name="untagSubgraph"> </a>
					<div class="fixedFont">
					
					
					<b>untagSubgraph</b>(node)
					
					</div>
					<div class="description">
						Untags a subgraph
						
							<br />
							<i>Defined in: </i> <a href="../symbols/src/geovision_src_geovision_static_js_navigation.js.html">navigation.js</a>.
						
						
					</div>
					
					
					
						
							<dl class="detailList">
							<dt class="heading">Parameters:</dt>
							
								<dt>
									<b>node</b>
									
								</dt>
								<dd>node to have its subgraph untagged</dd>
							
							</dl>
						
						
						
						
						
						
						

					<hr />
				
					<a name="updateBitscores"> </a>
					<div class="fixedFont">
					
					
					<b>updateBitscores</b>()
					
					</div>
					<div class="description">
						Function for updating data.bitscore field for all nodes in the graph.
Should be used after deleting edges from the graph if relevant values are not otherwise updated.
						
							<br />
							<i>Defined in: </i> <a href="../symbols/src/geovision_src_geovision_static_js_navigation.js.html">navigation.js</a>.
						
						
					</div>
					
					
					
						
						
						
						
						
						
						

					
				
			
			
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